{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T10:55:14Z","timestamp":1756896914291,"version":"3.37.3"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2018,4,6]],"date-time":"2018-04-06T00:00:00Z","timestamp":1522972800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Cluster of Excellence on Multimodal Computing and Interaction","award":["EXC284"],"award-info":[{"award-number":["EXC284"]}]},{"name":"German National Science Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genome-wide measurements of paired miRNA and gene expression data have enabled the prediction of competing endogenous RNAs (ceRNAs). It has been shown that the sponge effect mediated by protein-coding as well as non-coding ceRNAs can play an important regulatory role in the cell in health and disease. Therefore, many computational methods for the computational identification of ceRNAs have been suggested. In particular, methods based on Conditional Mutual Information (CMI) have shown promising results. However, the currently available implementation is slow and cannot be used to perform computations on a large scale.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present JAMI, a Java tool that uses a non-parametric estimator for CMI values from gene and miRNA expression data. We show that JAMI speeds up the computation of ceRNA networks by a factor of \u223c70 compared to currently available implementations. Further, JAMI supports multi-threading to make use of common multi-core architectures for further performance gain.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Requirements<\/jats:title>\n                  <jats:p>Java 8.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>JAMI is available as open-source software from https:\/\/github.com\/SchulzLab\/JAMI.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty221","type":"journal-article","created":{"date-parts":[[2018,4,4]],"date-time":"2018-04-04T19:12:36Z","timestamp":1522869156000},"page":"3050-3051","source":"Crossref","is-referenced-by-count":12,"title":["JAMI: fast computation of conditional mutual information for ceRNA network analysis"],"prefix":"10.1093","volume":"34","author":[{"given":"Andrea","family":"Hornakova","sequence":"first","affiliation":[{"name":"Max Planck Institute for Informatics, Saarland University, Saarland Informatics Campus, Saarbr\u00fccken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0941-4168","authenticated-orcid":false,"given":"Markus","family":"List","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Informatics, Saarland University, Saarland Informatics Campus, Saarbr\u00fccken, Germany"}]},{"given":"Jilles","family":"Vreeken","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Informatics, Saarland University, Saarland Informatics Campus, Saarbr\u00fccken, Germany"},{"name":"Cluster of Excellence MMCI, Saarland University, Saarland Informatics Campus, Saarbr\u00fccken, Germany"}]},{"given":"Marcel H","family":"Schulz","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Informatics, Saarland University, Saarland Informatics Campus, Saarbr\u00fccken, Germany"},{"name":"Cluster of Excellence MMCI, Saarland University, Saarland Informatics Campus, Saarbr\u00fccken, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,4,6]]},"reference":[{"key":"2023061313394600500_bty221-B1","doi-asserted-by":"crossref","first-page":"363.","DOI":"10.1038\/msb.2010.24","article-title":"Target mRNA abundance dilutes microRNA and siRNA activity","volume":"6","author":"Arvey","year":"2010","journal-title":"Mol. Syst. Biol"},{"key":"2023061313394600500_bty221-B2","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1101\/gr.178194.114","article-title":"Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks","volume":"25","author":"Chiu","year":"2015","journal-title":"Genome Research"},{"key":"2023061313394600500_bty221-B3","doi-asserted-by":"crossref","first-page":"418.","DOI":"10.1186\/s12864-017-3790-7","article-title":"High-throughput validation of ceRNA regulatory network","volume":"18","author":"Chiu","year":"2017","journal-title":"BMC Genomics"},{"key":"2023061313394600500_bty221-B4","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.1109\/18.761290","article-title":"Estimation of the information by an adaptive partitioning of the observation space","volume":"45","author":"Darbellay","year":"1999","journal-title":"IEEE Trans. Information Theory"},{"key":"2023061313394600500_bty221-B5","doi-asserted-by":"crossref","first-page":"1.","DOI":"10.1155\/2013\/360678","article-title":"Gene regulation, modulation, and their applications in gene expression data analysis","volume":"2013","author":"Flores","year":"2013","journal-title":"Adv. Bioinformatics"},{"key":"2023061313394600500_bty221-B6","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1101\/gr.082701.108","article-title":"Most mammalian mRNAs are conserved targets of microRNAs","volume":"19","author":"Friedman","year":"2009","journal-title":"Genome Res"},{"key":"2023061313394600500_bty221-B7","doi-asserted-by":"crossref","first-page":"D98","DOI":"10.1093\/nar\/gkn714","article-title":"miR2Disease: a manually curated database for microRNA deregulation in human disease","volume":"37","author":"Jiang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023061313394600500_bty221-B8","first-page":"577","article-title":"Computational methods for identifying miRNA sponge interactions","volume":"18","author":"Le","year":"2017","journal-title":"Brief. Bioinformatics"},{"key":"2023061313394600500_bty221-B9","first-page":"3859582","article-title":"Cancer-Related Triplets of mRNA-lncRNA-miRNA Revealed by Integrative Network in Uterine Corpus Endometrial Carcinoma","volume":"2017","author":"Liu","year":"2017","journal-title":"BioMed Res. Int"},{"key":"2023061313394600500_bty221-B10","doi-asserted-by":"crossref","first-page":"83.","DOI":"10.1186\/1752-0509-8-83","article-title":"Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer","volume":"8","author":"Paci","year":"2014","journal-title":"BMC Syst. Biol"},{"key":"2023061313394600500_bty221-B11","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1038\/nature09144","article-title":"A coding-independent function of gene and pseudogene mRNAs regulates tumour biology","volume":"465","author":"Poliseno","year":"2010","journal-title":"Nature"},{"key":"2023061313394600500_bty221-B12","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/j.cell.2011.07.014","article-title":"A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?","volume":"146","author":"Salmena","year":"2011","journal-title":"Cell"},{"key":"2023061313394600500_bty221-B13","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"2023061313394600500_bty221-B14","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/j.cell.2011.09.041","article-title":"An extensive MicroRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma","volume":"147","author":"Sumazin","year":"2011","journal-title":"Cell"},{"key":"2023061313394600500_bty221-B15","doi-asserted-by":"crossref","first-page":"344.","DOI":"10.1038\/nature12986","article-title":"The multilayered complexity of ceRNA crosstalk and competition","volume":"505","author":"Tay","year":"2014","journal-title":"Nature"},{"key":"2023061313394600500_bty221-B16","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","article-title":"Comprehensive molecular portraits of human breast tumours","volume":"490","author":"TCGA, T. C. G. A. C.","year":"2012","journal-title":"Nature"},{"key":"2023061313394600500_bty221-B17","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.molcel.2010.03.007","article-title":"Genome-wide dissection of microRNA functions and co-targeting networks using gene-set signatures","volume":"38","author":"Tsang","year":"2010","journal-title":"Mol. Cell"},{"key":"2023061313394600500_bty221-B18","doi-asserted-by":"crossref","first-page":"3478","DOI":"10.1093\/nar\/gkv233","article-title":"Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer","volume":"43","author":"Wang","year":"2015","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/3050\/50582523\/bioinformatics_34_17_3050.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/3050\/50582523\/bioinformatics_34_17_3050.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T13:41:42Z","timestamp":1686663702000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/17\/3050\/4962493"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,6]]},"references-count":18,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2018,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty221","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,9,1]]},"published":{"date-parts":[[2018,4,6]]}}}